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Yorodumi- PDB-7uvp: Cryo-EM structure of the ribosome-bound Bacteroides thetaiotaomic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7uvp | ||||||
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Title | Cryo-EM structure of the ribosome-bound Bacteroides thetaiotaomicron EF-G2 | ||||||
Components | Tetracycline resistance protein TetQTetracycline | ||||||
Keywords | TRANSLATION / Translation elongation factor / Bacteroides thetaiotaomicron EF-G2 | ||||||
Function / homology | Function and homology information ribosome disassembly / translation elongation factor activity / GTPase activity / GTP binding Similarity search - Function | ||||||
Biological species | Bacteroides thetaiotaomicron VPI-5482 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / Resolution: 3.7 Å | ||||||
Authors | Wang, C. / Han, W. / Groisman, E.A. / Liu, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Cryo-EM structure of the ribosome-bound Bacteroides thetaiotaomicron EF-G2 Authors: Wang, C. / Han, W. / Groisman, E.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uvp.cif.gz | 134.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uvp.ent.gz | 104.5 KB | Display | PDB format |
PDBx/mmJSON format | 7uvp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/7uvp ftp://data.pdbj.org/pub/pdb/validation_reports/uv/7uvp | HTTPS FTP |
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-Related structure data
Related structure data | 26815MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 80353.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria) Strain: ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50 Gene: BT_2167 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q8A5S1 |
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#2: Chemical | ChemComp-GTP / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: ribosome-bound Bacteroides thetaiotaomicron EF-G2 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria) |
Source (recombinant) | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: DIRECT ELECTRON DE-64 (8k x 8k) |
-Processing
Software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 210467 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.21 Å2 | ||||||||||||||||||||||||
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